def setUp(self):
self.builder = AtomListBuilder()
self._baseData = dict(
[
(u"_atom_site_fract_x", [u"1/8", u"0.34(1)"]),
(u"_atom_site_fract_y", [u"1/8", u"0.56(2)"]),
(u"_atom_site_fract_z", [u"1/8", u"0.23(2)"]),
]
)
class AtomListBuilderTest(unittest.TestCase):
def setUp(self):
self.builder = AtomListBuilder()
self._baseData = dict(
[
(u"_atom_site_fract_x", [u"1/8", u"0.34(1)"]),
(u"_atom_site_fract_y", [u"1/8", u"0.56(2)"]),
(u"_atom_site_fract_z", [u"1/8", u"0.23(2)"]),
]
)
def _getData(self, additionalData):
data = self._baseData.copy()
data.update(additionalData)
return data
def test_getAtoms_required_keys(self):
mandatoryKeys = dict(
[
(u"_atom_site_label", [u"Si"]),
(u"_atom_site_fract_x", [u"1/8"]),
(u"_atom_site_fract_y", [u"1/8"]),
(u"_atom_site_fract_z", [u"1/8"]),
]
)
for key in mandatoryKeys:
tmp = mandatoryKeys.copy()
del tmp[key]
self.assertRaises(RuntimeError, self.builder._getAtoms, cifData=tmp)
def test_getAtoms_correct(self):
data = self._getData(
dict(
[
(u"_atom_site_label", [u"Si", u"Al"]),
(u"_atom_site_occupancy", [u"0.6", u"0.4(0)"]),
(u"_atom_site_u_iso_or_equiv", [u"0.01", u"0.02"]),
]
)
)
self.assertEqual(self.builder._getAtoms(data), "Si 1/8 1/8 1/8 0.6 0.01;Al 0.34 0.56 0.23 0.4 0.02")
def test_getAtoms_atom_type_symbol(self):
data = self._getData(
dict(
[
(u"_atom_site_label", [u"Fake1", u"Fake2"]),
(u"_atom_site_occupancy", [u"1.0", u"1.0(0)"]),
(u"_atom_site_u_iso_or_equiv", [u"0.01", u"0.02"]),
]
)
)
self.assertEqual(self.builder._getAtoms(data), "Fake 1/8 1/8 1/8 1.0 0.01;Fake 0.34 0.56 0.23 1.0 0.02")
del data[u"_atom_site_label"]
data[u"_atom_site_type_symbol"] = [u"Si", u"Al"]
self.assertEqual(self.builder._getAtoms(data), "Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02")
def test_getAtoms_B_iso(self):
data = self._getData(
dict(
[
(u"_atom_site_label", [u"Si", u"Al"]),
(u"_atom_site_occupancy", [u"1.0", u"1.0(0)"]),
(u"_atom_site_b_iso_or_equiv", [u"1.0", u"2.0"]),
]
)
)
# python 2 & 3 convert float to str with different precision
if sys.version_info[0] < 3:
self.assertEqual(
self.builder._getAtoms(data), "Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0 0.0253302959106"
)
else:
self.assertEqual(
self.builder._getAtoms(data),
"Si 1/8 1/8 1/8 1.0 0.012665147955292222;Al 0.34 0.56 0.23 1.0 0.025330295910584444",
)
def test_getAtoms_no_occupancy(self):
data = self._getData(
dict([(u"_atom_site_label", [u"Si", u"Al"]), (u"_atom_site_u_iso_or_equiv", [u"0.01", u"0.02"])])
)
self.assertEqual(self.builder._getAtoms(data), "Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02")
def test_getAtoms_no_u_or_b(self):
data = self._getData(
dict([(u"_atom_site_label", [u"Si", u"Al"]), (u"_atom_site_occupancy", [u"1.0", u"1.0(0)"])])
)
self.assertEqual(self.builder._getAtoms(data), "Si 1/8 1/8 1/8 1.0;Al 0.34 0.56 0.23 1.0")
def test_getAtoms_invalid_u(self):
data = self._getData(
dict(
[
(u"_atom_site_label", [u"Si", u"Al"]),
(u"_atom_site_occupancy", [u"1.0", u"1.0(0)"]),
(u"_atom_site_u_iso_or_equiv", [u"0.01", u"sdfsdfs"]),
]
)
)
self.assertEqual(self.builder._getAtoms(data), "Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0")
def test_getAtoms_invalid_b(self):
data = self._getData(
dict(
[
(u"_atom_site_label", [u"Si", u"Al"]),
(u"_atom_site_occupancy", [u"1.0", u"1.0(0)"]),
(u"_atom_site_b_iso_or_equiv", [u"1.0", u"sdfsdfs"]),
]
)
)
# python 2 & 3 convert float to str with different precision
if sys.version_info[0] < 3:
self.assertEqual(self.builder._getAtoms(data), "Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0")
else:
self.assertEqual(
self.builder._getAtoms(data), "Si 1/8 1/8 1/8 1.0 0.012665147955292222;Al 0.34 0.56 0.23 1.0"
)
def test_getAtoms_aniso_u_orthogonal(self):
uElements = {
"11": [u"0.01", u"0.02"],
"12": [u"0.0", u"0.0"],
"13": [u"0.0", u"0.0"],
"22": [u"0.01", u"0.02"],
"23": [u"0.0", u"0.0"],
"33": [u"0.04", u"0.05"],
}
uDict = dict([(u"_atom_site_aniso_u_{0}".format(key), value) for key, value in iteritems(uElements)])
uDict.update(dict([(u"_atom_site_label", [u"Si", u"Al"]), (u"_atom_site_aniso_label", [u"Si", u"Al"])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
# u_equiv should be (0.01 + 0.01 + 0.04)/3 = 0.02 and (0.2 + 0.2 + 0.5)/3 = 0.03
self.assertEqual(self.builder._getAtoms(data, cell), "Si 1/8 1/8 1/8 1.0 0.02;Al 0.34 0.56 0.23 1.0 0.03")
def test_getAtoms_aniso_u_hexagonal(self):
uElements = {
"11": [u"0.01", u"0.02"],
"12": [u"0.01", u"0.01"],
"13": [u"0.0", u"0.0"],
"22": [u"0.01", u"0.02"],
"23": [u"0.0", u"0.0"],
"33": [u"0.04", u"0.05"],
}
uDict = dict([(u"_atom_site_aniso_u_{0}".format(key), value) for key, value in iteritems(uElements)])
uDict.update(dict([(u"_atom_site_label", [u"Si", u"Al"]), (u"_atom_site_aniso_label", [u"Si", u"Al"])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2, 90, 90, 120)
# u_equiv should be (4/3*(0.01 + 0.01 - 0.01) + 0.04)/3 = 0.0177... and (4/3*(0.02 + 0.02 - 0.01) + 0.05)/3 = 0.03
self.assertEqual(self.builder._getAtoms(data, cell), "Si 1/8 1/8 1/8 1.0 0.01778;Al 0.34 0.56 0.23 1.0 0.03")
def test_getAtoms_aniso_b_orthogonal(self):
bElements = {
"11": [u"1.0", u"2.0"],
"12": [u"0.0", u"0.0"],
"13": [u"0.0", u"0.0"],
"22": [u"1.0", u"2.0"],
"23": [u"0.0", u"0.0"],
"33": [u"4.0", u"5.0"],
}
bDict = dict([(u"_atom_site_aniso_b_{0}".format(key), value) for key, value in iteritems(bElements)])
bDict.update(dict([(u"_atom_site_label", [u"Si", u"Al"]), (u"_atom_site_aniso_label", [u"Si", u"Al"])]))
data = self._getData(bDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell), "Si 1/8 1/8 1/8 1.0 0.02533;Al 0.34 0.56 0.23 1.0 0.038")
def test_getAtoms_aniso_iso_mixed(self):
uElements = {"11": [u"0.01"], "12": [u"0.0"], "13": [u"0.0"], "22": [u"0.01"], "23": [u"0.0"], "33": [u"0.04"]}
uDict = dict([(u"_atom_site_aniso_u_{0}".format(key), value) for key, value in iteritems(uElements)])
uDict.update(
dict(
[
(u"_atom_site_label", [u"Si", u"Al"]),
(u"_atom_site_aniso_label", [u"Al"]),
(u"_atom_site_u_iso_or_equiv", [u"0.01", u"invalid"]),
]
)
)
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell), "Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02")
def test_getAtoms_iso_preferred(self):
uElements = {
"11": [u"0.01", u"0.02"],
"12": [u"0.0", u"0.0"],
"13": [u"0.0", u"0.0"],
"22": [u"0.01", u"0.02"],
"23": [u"0.0", u"0.0"],
"33": [u"0.04", u"0.05"],
}
uDict = dict([(u"_atom_site_aniso_u_{0}".format(key), value) for key, value in iteritems(uElements)])
uDict.update(
dict(
[
(u"_atom_site_label", [u"Si", u"Al"]),
(u"_atom_site_aniso_label", [u"Si", u"Al"]),
(u"_atom_site_u_iso_or_equiv", [u"0.01", u"0.02"]),
]
)
)
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell), "Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02")
def test_getReciprocalLengthMatrix(self):
cell = UnitCell(1, 2, 3)
matrix = self.builder._getReciprocalLengthSquaredMatrix(cell)
expected = np.array(
[
[(1.0 / 1.0 * 1.0 / 1.0), (1.0 / 1.0 * 1.0 / 2.0), (1.0 / 1.0 * 1.0 / 3.0)],
[(1.0 / 2.0 * 1.0 / 1.0), (1.0 / 2.0 * 1.0 / 2.0), (1.0 / 2.0 * 1.0 / 3.0)],
[(1.0 / 3.0 * 1.0 / 1.0), (1.0 / 3.0 * 1.0 / 2.0), (1.0 / 3.0 * 1.0 / 3.0)],
]
)
self.assertTrue(np.all(matrix == expected))
def test_getSumWeights_orthorhombic(self):
cell = UnitCell(1, 2, 3, 90, 90, 90)
matrix = self.builder._getMetricDependentWeights(cell)
expected = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
self.assertTrue(np.all(np.abs(matrix - expected) < 1.0e-9))
def test_getSumWeights_hexagonal(self):
cell = UnitCell(2, 2, 3, 90, 90, 120)
matrix = self.builder._getMetricDependentWeights(cell)
expected = np.array([[4.0 / 3.0, -2.0 / 3.0, 0.0], [-2.0 / 3.0, 4.0 / 3.0, 0.0], [0.0, 0.0, 1.0]])
self.assertTrue(np.all(np.abs(matrix - expected) < 1.0e-9))
def setUp(self):
self.builder = AtomListBuilder()
self._baseData = dict([(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
class AtomListBuilderTest(unittest.TestCase):
def setUp(self):
self.builder = AtomListBuilder()
self._baseData = dict([(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
def _getData(self, additionalData):
data = self._baseData.copy()
data.update(additionalData)
return data
def test_getAtoms_required_keys(self):
mandatoryKeys = dict([(u'_atom_site_label', [u'Si']),
(u'_atom_site_fract_x', [u'1/8']),
(u'_atom_site_fract_y', [u'1/8']),
(u'_atom_site_fract_z', [u'1/8'])])
for key in mandatoryKeys:
tmp = mandatoryKeys.copy()
del tmp[key]
self.assertRaises(RuntimeError,
self.builder._getAtoms,
cifData=tmp)
def test_getAtoms_correct(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'0.6', u'0.4(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 0.6 0.01;Al 0.34 0.56 0.23 0.4 0.02')
def test_getAtoms_atom_type_symbol(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Fake1', u'Fake2']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(
self.builder._getAtoms(data),
'Fake 1/8 1/8 1/8 1.0 0.01;Fake 0.34 0.56 0.23 1.0 0.02')
del data[u'_atom_site_label']
data[u'_atom_site_type_symbol'] = [u'Si', u'Al']
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_B_iso(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_b_iso_or_equiv', [u'1.0', u'2.0'])]))
self.assertEqual(
self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0 0.0253302959106'
)
def test_getAtoms_no_occupancy(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_no_u_or_b(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0;Al 0.34 0.56 0.23 1.0')
def test_getAtoms_invalid_u(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'sdfsdfs'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0')
def test_getAtoms_invalid_b(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_b_iso_or_equiv', [u'1.0', u'sdfsdfs'])]))
self.assertEqual(
self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0')
def test_getAtoms_aniso_u_orthogonal(self):
uElements = {
'11': [u'0.01', u'0.02'],
'12': [u'0.0', u'0.0'],
'13': [u'0.0', u'0.0'],
'22': [u'0.01', u'0.02'],
'23': [u'0.0', u'0.0'],
'33': [u'0.04', u'0.05']
}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value)
for key, value in uElements.iteritems()])
uDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
# u_equiv should be (0.01 + 0.01 + 0.04)/3 = 0.02 and (0.2 + 0.2 + 0.5)/3 = 0.03
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.02;Al 0.34 0.56 0.23 1.0 0.03')
def test_getAtoms_aniso_u_hexagonal(self):
uElements = {
'11': [u'0.01', u'0.02'],
'12': [u'0.01', u'0.01'],
'13': [u'0.0', u'0.0'],
'22': [u'0.01', u'0.02'],
'23': [u'0.0', u'0.0'],
'33': [u'0.04', u'0.05']
}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value)
for key, value in uElements.iteritems()])
uDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2, 90, 90, 120)
# u_equiv should be (4/3*(0.01 + 0.01 - 0.01) + 0.04)/3 = 0.0177... and (4/3*(0.02 + 0.02 - 0.01) + 0.05)/3 = 0.03
self.assertEqual(
self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.01778;Al 0.34 0.56 0.23 1.0 0.03')
def test_getAtoms_aniso_b_orthogonal(self):
bElements = {
'11': [u'1.0', u'2.0'],
'12': [u'0.0', u'0.0'],
'13': [u'0.0', u'0.0'],
'22': [u'1.0', u'2.0'],
'23': [u'0.0', u'0.0'],
'33': [u'4.0', u'5.0']
}
bDict = dict([(u'_atom_site_aniso_b_{0}'.format(key), value)
for key, value in bElements.iteritems()])
bDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])]))
data = self._getData(bDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(
self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.02533;Al 0.34 0.56 0.23 1.0 0.038')
def test_getAtoms_aniso_iso_mixed(self):
uElements = {
'11': [u'0.01'],
'12': [u'0.0'],
'13': [u'0.0'],
'22': [u'0.01'],
'23': [u'0.0'],
'33': [u'0.04']
}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value)
for key, value in uElements.iteritems()])
uDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Al']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'invalid'])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_iso_preferred(self):
uElements = {
'11': [u'0.01', u'0.02'],
'12': [u'0.0', u'0.0'],
'13': [u'0.0', u'0.0'],
'22': [u'0.01', u'0.02'],
'23': [u'0.0', u'0.0'],
'33': [u'0.04', u'0.05']
}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value)
for key, value in uElements.iteritems()])
uDict.update(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getReciprocalLengthMatrix(self):
cell = UnitCell(1, 2, 3)
matrix = self.builder._getReciprocalLengthSquaredMatrix(cell)
expected = np.array([[(1.0 / 1.0 * 1.0 / 1.0), (1.0 / 1.0 * 1.0 / 2.0),
(1.0 / 1.0 * 1.0 / 3.0)],
[(1.0 / 2.0 * 1.0 / 1.0), (1.0 / 2.0 * 1.0 / 2.0),
(1.0 / 2.0 * 1.0 / 3.0)],
[(1.0 / 3.0 * 1.0 / 1.0), (1.0 / 3.0 * 1.0 / 2.0),
(1.0 / 3.0 * 1.0 / 3.0)]])
self.assertTrue(np.all(matrix == expected))
def test_getSumWeights_orthorhombic(self):
cell = UnitCell(1, 2, 3, 90, 90, 90)
matrix = self.builder._getMetricDependentWeights(cell)
expected = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0,
1.0]])
self.assertTrue(np.all(np.abs(matrix - expected) < 1.e-9))
def test_getSumWeights_hexagonal(self):
cell = UnitCell(2, 2, 3, 90, 90, 120)
matrix = self.builder._getMetricDependentWeights(cell)
expected = np.array([[4. / 3., -2. / 3., 0.0],
[-2. / 3., 4. / 3., 0.0], [0.0, 0.0, 1.0]])
self.assertTrue(np.all(np.abs(matrix - expected) < 1.e-9))
def setUp(self):
self.builder = AtomListBuilder()
self._baseData = dict([
(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
class AtomListBuilderTest(unittest.TestCase):
def setUp(self):
self.builder = AtomListBuilder()
self._baseData = dict([
(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
def _getData(self, additionalData):
data = self._baseData.copy()
data.update(additionalData)
return data
def test_getAtoms_required_keys(self):
mandatoryKeys = dict([(u'_atom_site_label', [u'Si']),
(u'_atom_site_fract_x', [u'1/8']),
(u'_atom_site_fract_y', [u'1/8']),
(u'_atom_site_fract_z', [u'1/8'])])
for key in mandatoryKeys:
tmp = mandatoryKeys.copy()
del tmp[key]
self.assertRaises(RuntimeError, self.builder._getAtoms, cifData=tmp)
def test_getAtoms_correct(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'0.6', u'0.4(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 0.6 0.01;Al 0.34 0.56 0.23 0.4 0.02')
def test_getAtoms_atom_type_symbol(self):
data = self._getData(dict([(u'_atom_site_label', [u'Fake1', u'Fake2']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data), 'Fake 1/8 1/8 1/8 1.0 0.01;Fake 0.34 0.56 0.23 1.0 0.02')
del data[u'_atom_site_label']
data[u'_atom_site_type_symbol'] = [u'Si', u'Al']
self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_B_iso(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_b_iso_or_equiv', [u'1.0', u'2.0'])]))
# python 2 & 3 convert float to str with different precision
if sys.version_info[0] < 3:
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0 0.0253302959106')
else:
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.012665147955292222;Al 0.34 0.56 0.23 1.0 0.025330295910584444')
def test_getAtoms_no_occupancy(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_no_u_or_b(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0;Al 0.34 0.56 0.23 1.0')
def test_getAtoms_invalid_u(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'sdfsdfs'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0')
def test_getAtoms_invalid_b(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_b_iso_or_equiv', [u'1.0', u'sdfsdfs'])]))
# python 2 & 3 convert float to str with different precision
if sys.version_info[0] < 3:
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0')
else:
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.012665147955292222;Al 0.34 0.56 0.23 1.0')
def test_getAtoms_aniso_u_orthogonal(self):
uElements = {'11': [u'0.01', u'0.02'], '12': [u'0.0', u'0.0'], '13': [u'0.0', u'0.0'], '22': [u'0.01', u'0.02'],
'23': [u'0.0', u'0.0'], '33': [u'0.04', u'0.05']}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value) for key, value in iteritems(uElements)])
uDict.update(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])
]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
# u_equiv should be (0.01 + 0.01 + 0.04)/3 = 0.02 and (0.2 + 0.2 + 0.5)/3 = 0.03
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.02;Al 0.34 0.56 0.23 1.0 0.03')
def test_getAtoms_aniso_u_hexagonal(self):
uElements = {'11': [u'0.01', u'0.02'], '12': [u'0.01', u'0.01'], '13': [u'0.0', u'0.0'],
'22': [u'0.01', u'0.02'],
'23': [u'0.0', u'0.0'], '33': [u'0.04', u'0.05']}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value) for key, value in iteritems(uElements)])
uDict.update(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])
]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2, 90, 90, 120)
# u_equiv should be (4/3*(0.01 + 0.01 - 0.01) + 0.04)/3 = 0.0177... and (4/3*(0.02 + 0.02 - 0.01) + 0.05)/3 = 0.03
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.01778;Al 0.34 0.56 0.23 1.0 0.03')
def test_getAtoms_aniso_b_orthogonal(self):
bElements = {'11': [u'1.0', u'2.0'], '12': [u'0.0', u'0.0'], '13': [u'0.0', u'0.0'],
'22': [u'1.0', u'2.0'], '23': [u'0.0', u'0.0'], '33': [u'4.0', u'5.0']}
bDict = dict([(u'_atom_site_aniso_b_{0}'.format(key), value) for key, value in iteritems(bElements)])
bDict.update(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al'])
]))
data = self._getData(bDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.02533;Al 0.34 0.56 0.23 1.0 0.038')
def test_getAtoms_aniso_iso_mixed(self):
uElements = {'11': [u'0.01'], '12': [u'0.0'], '13': [u'0.0'], '22': [u'0.01'],
'23': [u'0.0'], '33': [u'0.04']}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value) for key, value in iteritems(uElements)])
uDict.update(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Al']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'invalid'])
]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_iso_preferred(self):
uElements = {'11': [u'0.01', u'0.02'], '12': [u'0.0', u'0.0'], '13': [u'0.0', u'0.0'],
'22': [u'0.01', u'0.02'], '23': [u'0.0', u'0.0'], '33': [u'0.04', u'0.05']}
uDict = dict([(u'_atom_site_aniso_u_{0}'.format(key), value) for key, value in iteritems(uElements)])
uDict.update(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_aniso_label', [u'Si', u'Al']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])
]))
data = self._getData(uDict)
cell = UnitCell(5.4, 4.3, 3.2)
self.assertEqual(self.builder._getAtoms(data, cell),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getReciprocalLengthMatrix(self):
cell = UnitCell(1, 2, 3)
matrix = self.builder._getReciprocalLengthSquaredMatrix(cell)
expected = np.array([[(1.0 / 1.0 * 1.0 / 1.0), (1.0 / 1.0 * 1.0 / 2.0), (1.0 / 1.0 * 1.0 / 3.0)],
[(1.0 / 2.0 * 1.0 / 1.0), (1.0 / 2.0 * 1.0 / 2.0), (1.0 / 2.0 * 1.0 / 3.0)],
[(1.0 / 3.0 * 1.0 / 1.0), (1.0 / 3.0 * 1.0 / 2.0), (1.0 / 3.0 * 1.0 / 3.0)]])
self.assertTrue(np.all(matrix == expected))
def test_getSumWeights_orthorhombic(self):
cell = UnitCell(1, 2, 3, 90, 90, 90)
matrix = self.builder._getMetricDependentWeights(cell)
expected = np.array([[1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
self.assertTrue(np.all(np.abs(matrix - expected) < 1.e-9))
def test_getSumWeights_hexagonal(self):
cell = UnitCell(2, 2, 3, 90, 90, 120)
matrix = self.builder._getMetricDependentWeights(cell)
expected = np.array([[4. / 3., -2. / 3., 0.0],
[-2. / 3., 4. / 3., 0.0],
[0.0, 0.0, 1.0]])
self.assertTrue(np.all(np.abs(matrix - expected) < 1.e-9))
